10-23192716-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_178161.3(PTF1A):c.186C>T(p.Tyr62=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000321 in 1,556,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
PTF1A
NM_178161.3 synonymous
NM_178161.3 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 4.35
Genes affected
PTF1A (HGNC:23734): (pancreas associated transcription factor 1a) This gene encodes a protein that is a component of the pancreas transcription factor 1 complex (PTF1) and is known to have a role in mammalian pancreatic development. The protein plays a role in determining whether cells allocated to the pancreatic buds continue towards pancreatic organogenesis or revert back to duodenal fates. The protein is thought to be involved in the maintenance of exocrine pancreas-specific gene expression including elastase 1 and amylase. Mutations in this gene cause cerebellar agenesis and loss of expression is seen in ductal type pancreas cancers. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 10-23192716-C-T is Benign according to our data. Variant chr10-23192716-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1914944.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTF1A | NM_178161.3 | c.186C>T | p.Tyr62= | synonymous_variant | 1/2 | ENST00000376504.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTF1A | ENST00000376504.4 | c.186C>T | p.Tyr62= | synonymous_variant | 1/2 | 1 | NM_178161.3 | P1 | |
PTF1A | ENST00000638469.1 | c.114+39C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151956Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
1
AN:
151956
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000285 AC: 4AN: 1404790Hom.: 0 Cov.: 33 AF XY: 0.00000143 AC XY: 1AN XY: 698266
GnomAD4 exome
AF:
AC:
4
AN:
1404790
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
698266
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151956Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74224
GnomAD4 genome
AF:
AC:
1
AN:
151956
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74224
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 21, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at